Hi Dr. Simmerling,
Thank you. Yes I am aware of the issues you mentioned in the last
reply. I am interested in structures in vacuum, so we think high
temperatures are needed to explore different conformations.
Thank you,
Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
> Dan Roe can probably answer about the error- but are you sure you want to
> run at 2100K? There are many, many things that can go wrong in simulations
> at such a high T, and it's not clear that it's needed.
>
> just want to make sure you know what you're doing, if you are aware of the
> issues then it's fine of course!
>
>
> On Wed, Jun 15, 2011 at 9:49 AM, <tdo.chem.ucsb.edu> wrote:
>
>> Hi,
>>
>> I am running REMD and use ptraj to extract trajectories from mdcrd outputs.
>>
>> Here is the script
>>
>> trajin ./remd.00 remdtraj remdtrajtemp 300.0
>> trajout traj300K.dat pdb append
>>
>> It works fine until recently I get some messages:
>>
>> REMDTRAJ: Final repTemp value read= 1043.840000, set 302
>> Could not find target 300.000000 in any of the replica trajectories.
>> Check that all replica trajectory files were found and that
>> none of the trajectories are corrupted (e.g. missing a temperature).
>> ptrajProcessInputCoordinates(): Target replica temperature not found
>> in traj! 100%
>>
>>
>> PTRAJ: Successfully read in 301 sets and processed 301 sets.
>>
>>
>> It only happens to 2/5 of my simulations that I am running (5
>> different systems using identical method). It seems that ptraj can
>> only read 300/450 sets of trajectories. So I wonder if this happens
>> due to something wrong in my simulations, or ptraj itself.
>>
>> My simulation has max temp ~ 2100K, in vacuum.
>>
>>
>> Thanks,
>>
>>
>>
>> --
>> Thanh D. Do
>> Department of Chemistry & Biochemistry
>> University of California Santa Barbara
>> Santa Barbara, California, 93106
>>
>>
>>
>>
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--
Thanh D. Do
Department of Chemistry & Biochemistry
University of California Santa Barbara
Santa Barbara, California, 93106
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Received on Wed Jun 15 2011 - 07:00:05 PDT
